Do you have an audio probe? If not, make one. Then use it "listen" to the circuit at key points. I'd be interested in what you hear:
(1) just after the op amp output (before the clipping diodes)
(2) after the clipping diodes and before the tone control
(3) after the tone control
I bet if you probe the circuit, you will find the spot where the bass frequencies are disappearing. In fact, check the signal right before the op amp - is something strange happening there?
And, as always, check all of your components and make sure the resistor and capacitor values are what they should be (use the schematic as a reference for this).
Good luck!